nfable,
Sorry, I'm not sure I understand your question. I'm guessing that you want to make some sort of annotation to your file? I have never seen or used the "note tool" in Photoshop but I have used the annotation tool in Acrobat. Is it like that? In Photoshop I usually just add metadata by going under File/File info. You can do this as well in Illustrator. Maybe I've just never used the note tool or maybe it is a new tool in CS 5.5? I don't have CS 5.5 so I wouldn't know.
If adding metadata isn't what you want and you actually want a message that you can see when you open the file, then I would suggest that when you add a new layer in Illustrator (a new layer after the 1st layer), you are given some options (template, show, preview, lock, print, dim images to ....). If you uncheck the "print" option, the layer will not print and then you can add a message or a note but it will not print (but you can see it). Some design agencies do this and then add their tracking information, etc some where off the art board for reference.
I hope this helps.